Staphylococcus peptides for bacterial interference

ABSTRACT

The present invention provides a cyclic peptide comprising the structure: 
                 
 
wherein X is selected from the group consisting of an amino acid, an amino acid analog, a peptidomimetic and a non-amide isostere, Z is selected from the group consisting of a synthetic amino acid and a biosynthetic amino acid, R is selected from the group consisting of oxygen, nitrogen, sulfur and carbon, n is 0 to 10 and y is 1 to 10. The present invention also provides a cyclic peptide comprising the amino acid sequence of NH 2 —X (n) -Z-X (y) —COOH and a cyclic bond between the Z residue and COOH other than a thioester bond, wherein X is selected from the group consisting of an amino acid, an amino acid analog, a peptidomimetic and a non-amide isostere, Z is selected from the group consisting of a synthetic amino acid and a biosynthetic amino acid, n is 0 to 10 and y is 1 to 10. Methods of preparation including a cyclization protocol, and methods of use of the cyclic peptides of the invention are also disclosed.

CROSS REFERENCE TO RELATED APPLICATIONS

The present application is a Continuation of application Ser. No.09/339,511, filed Jun. 24, 1999 now U.S. Pat. No. 6,337,385, which, inturn, claims priority under 35 U.S.C. § 119(e) from ProvisionalApplication Ser. No. 60/090,402, filed Jun. 24, 1998. The disclosures ofboth applications are incorporated herein by reference in theirentirety.

Throughout this application, various publications are referenced byauthor and date. Full citations for these publications may be foundlisted alphabetically at the end of the specification immediatelyfollowing the Sequence Listing and the claims. The disclosures of thesepublications in their entireties are hereby incorporated by referenceinto this application in order to more fully describe the state of theart. The Sequence Listing is provided following the list of referencesand before the claims.

FIELD OF THE INVENTION

The present invention relates generally to synthetic, cyclic peptidesfor bacterial interference.

BACKGROUND OF THE INVENTION

Staphylococcus aureus (S. aureus) is an important pathogen in humanswhich is now under increasing risk of developing antibiotic resistanceto currently available therapeutics. Consequently, there is a pressingneed to identify new types of antibiotic agents effective against thesedrug resistant bacterial strains. The phenomenon of ‘bacterialinterference’ may provide as yet unexplored avenues for the design ofthese new therapeutics. Bacterial interference refers to the ability ofone organism to disrupt the biological functions of another. Untilrecently this survival process was thought to occur solely through agrowth inhibition mechanism (Ji, G., et al., 1997), however a novel typeof bacterial interference in S. aureus has been described which involvesthe inhibition of the so-called agr response (Novick, R. P., et al.,1993. Morfeldt. E., et al., 1995). This process is mediated by shortsecreted peptides containing a putative thiololactone ring structure.Chemical synthesis confirms that the native Agr peptides contain athiololactone moiety, and that this structure is absolutely necessaryfor full biological activity. In addition, structure-activity studiesare described by the present invention which offer insights into thenature of the agr activation and inhibition mechanisms.

Accessory genes allow bacteria to survive and multiply in plant oranimal hosts. In S. aureus these virulence factors (cytotoxins andtissue-degrading enzymes) are under the control of the agr locus whichcontains two divergent promoters, P2 and P3. The RNA transcript from theP3 promoter is responsible for the upregulation of secreted virulencefactors as well as the downregulation of surface proteins, the agrresponse (Novick, R. P., et al., 1993. Morfeldt, E., et al., 1995).There are four genes agrA-D, in the P2 operon which code for thecytosolic, transmembrane and extracellular components of adensity-sensing/autoinduction circuit (Novick, R. P., et al., 1995). Theproduct of the agrD gene is a pro-peptide which is processed andsecreted through AgrB, an integral membrane protein. The active AgrDpeptide is then thought to bind to the transmembrane receptor coded bythe agrC gene. Binding of the AgrD peptide triggers a standardtwo-component signal transduction pathway in which the AgrC receptorbecomes autophosphorylated on a histidine residue leading to subsequenttrans-phosphorylation of the AgrA gene product. Phosphorylated AgrA thenactivates the transcription from the P2 and P3 agr promoters (Novick, R.P., et al., 1995).

S. aureus strains can be divided into a least three groups (Ji, G., etal., 1997), each of whose secreted AgrD peptide can activate the agrresponse within the same group and inhibit the agr response in strainsbelonging to the other groups. It is the latter effect that constitutesa novel form of bacterial interference (Ji, G., et al., 1997). The AgrDautoinducing peptides, generated following processing and secretionthrough AgrB, consist of seven to nine residues. Interestingly, thesequences are highly variable among the groups, although all contain aconserved cysteine residue 5 amino acids—from the C-terminus. Massspectrometric analysis of AgrD peptides isolated from culturesupernatants indicated a mass discrepancy of −18 Da compared to thepredicted masses based on the peptide sequences (Ji, G., et al., 1995).This observation combined with the presence of the conserved cysteineresidue in AgrD peptides, has led to the suggestion that these secretedpeptides contain an intramolecular thiol ester linkage between thecysteine sulfliydryl group and the carboxy-terminus (Ji, G., et al.,1997). Consistent with this thiololactone structure, the addition ofhydroxylamine to a purified AgrD peptide was observed to abolish itsbiological activity (Ji, G., et al., 1997).

The inability to isolate significant quantities of secreted AgrDpeptides means that very little is known about the biochemistry of theAgrD/AgrC interaction. For example, the potency of the AgrD peptide ineither activating (within S. aureus strains of the same group) orinhibiting (in S. aureus strains from other groups) the agr response isunknown. Equally, it is essential to determine whether the putativethiololactone structure within the AgrD peptides is required foractivation of the agr response, inhibition of the agr response or both.The present disclosre provides such elucidation. This study detailedherein confirms the presence of the thiololactone moiety within the AgrDpeptides through total chemical synthesis. Having demonstrated syntheticaccess to the system, more rigorous biochemical and structure-activitystudies on the AgrD/AgrC interaction are addressed. The presentdisclosure further delineates that elimination of the thiol estercomponent of the cyclic ring structure can destroy activity activatingthe agr response while preserving (and enhancing) inhibitory activity.

SUMMARY OF THE INVENTION

The present invention provides a cyclic peptide comprising thestructure:

wherein X is selected from the group consisting of an amino acid, anamino acid analog, a peptidomimetic and a non-amide isostere, Z isselected from the group consisting of a synthetic amino acid and abiosynthetic amino acid, R is selected from the group consisting ofoxygen, nitrogen, sulfur and carbon, n is 0 to 10 and y is 1 to 10. Theinvention also contemplates a peptide composition comprising theprovided cyclic peptide and a carrier.

The present invention also provides a cyclic peptide comprising theamino acid sequence of NH₂—X_((n))-Z-X_((y))—COOH and a cyclic bondbetween the Z residue and COOH other than a thioester bond, wherein X isselected from the group consisting of an amino acid, an amino acidanalog, a peptidomimetic and a non-amide isostere, Z is selected fromthe group consisting of a synthetic amino acid and a biosynthetic aminoacid, n is 0 to 10 and y is 1 to 10. The invention also contemplates apeptide composition comprising the provided cyclic peptide and acarrier, as well as therapeutic methods for treatment of infection thatinvolve the administration of the pharmaceutical compositions that areand may be prepared in accordance with the teachings of the inventionherein. Yet further, the invention extends to methods for thepreparation of the cyclic peptide involving a cyclization protocol thatis described in further detail herein and is illustrated in Example 1and in FIG. 1A, and that itself is inventive.

Accordingly, it is a principal object of the present invention toprovide a cyclic peptide comprising the amino acid sequence ofNH₂—X_((n))-Z-X_((y))—COOH and a cyclic bond bond between the Z residueand COOH other than a thioester bond, wherein wherein X is selected fromthe group consisting of an amino acid, an amino acid analog, apeptidomimetic and a non-amide isostere, Z is selected from the groupconsisting of a synthetic amino acid and a biosynthetic amino acid, n is0 to 10 and y is 1 to 10.

It is a further object of the present invention to provide a cyclicpeptide comprising the amino acid sequence of NH₂—X_((n))-Z-X_((y))—COOHand a cyclic bond between the Z residue and COOH other than a thioesterbond, wherein X is selected from the group consisting of an amino acid,an amino acid analog, a peptidomimetic and a non-amide isostere, Z isselected from the group consisting of a synthetic amino acid and abiosynthetic amino acid, n is 0 to 10 and y is 1 to 10, that is devoidof activating activity and which retains inhibitory activity.

It is yet a further object of the present invention to provide a cyclicpeptide comprising the amino acid sequence of NH₂—X_((n))-Z-X_((y))—COOHand a cyclic bond between the Z residue and COOH other than a thioesterbond, wherein X is selected from the group consisting of an amino acid,an amino acid analog, a peptidomimetic and a non-amide isostere Z isselected from the group consisting of a synthetic amino acid and abiosynthetic amino acid, n is 0 to 10 and y is 1 to 10, wherein the bondis a selected from the group consisting of a lactam ring and a lactonering.

It is a still further object of the present invention to provide apharmaceutical composition which comprises the provided peptides and apharmaceutically acceptable carrier.

It is yet another object of the present invention to provide a methodfor the treatment of an S. aureus infection in a subject comprisingadministering to the subjects the provided pharmaceutical composition inan amount effective to treat the infection in the subject.

It is a still further object of the invention to provide methods for thepreparation of the cyclic peptides of the invention that involve a solidphase cyclization protocol as illustrated and described herein.

Other objects and advantages will become apparent to those skilled inthe art from a review of the ensuing description which proceeds withreference to the following illustrative drawings.

BRIEF DESCRIPTION OF THE FIGURES

FIGS. 1A-1C. Chemical synthesis of AgrD autoinducing peptides. FIG. 1A.Generation of thiololactone peptides via a solid phase intramolecularchemical ligation strategy. FIG. 1B. Reverse-phase HPLC of the crudereaction mixture from the AgrDI peptide synthesis. Inset shows theelectrospray, mass spectrum (ESMS) obtained from the major component inthe mixture: Expected mass for the AgrDI thiololactone=962.374 Da (961.9mass). FIG. 1C. Reverse-phase HPLC of the crude AgrDII reaction mixture.Inset shows the ESMS of the major component in the mixture: expectedmass for the AgrDII thiololactone=880.0129 Da (879.9 mass). Both HPLCspectra were obtained using a linear gradient of 0-73% buffer B over 30minutes (buffer B=CH3CN: H20: trifluoracetic acid: 90:10:1). ESMS wasperformed on a PE-Sciex API-100 single-quadrupole electrospray massspectrometer. Calculated masses were-obtained using the programMacProMass (Sunil Vemuri and Terry Lee, City of Hope. Duarte, Calif.).

FIGS. 2A-2C. Synthetic thiololactone peptides are biologically active.FIG. 2A and FIG. 2B show representative data for activation andinhibition respectively, of the agr response by a syntheticthiololactone peptide. Degree of activation/inhibition of the agrresponse, based on β-lactamase activity (see Table 1), is shown as aplot of Vmax versus peptide concentration. FIG. 2A. Activation of theagr response in group II S. aureus cells by synthetic AgrDII. FIG. 2B.Inhibition of the agr response in group I S. aureus cells by syntheticAgrDII. FIG. 2C. Effect of replacing each residue within the AgrDIIsequence with alanine on activation and inhibition activity.

FIGS. 3A-B. Proposed model for the activation and the inhibition of theagr response. FIG. 3A. Activation of the agr response occurs via anintra-class interaction in which a self AgrD peptide interacts with aself AgrC receptor. Specific AgrD/AgrC interactions lead to properpositioning of the peptide to undergo transacylation with a nucleophilewithin the receptor, leading to a signal-transducing conformationalchange. FIG. 3B. Inhibition of the agr response occurs via aninter-class, non-covalent interaction which serves to exclude thestrain's own activating peptide from the receptor. This interaction isalso specific.

DETAILED DESCRIPTION

The present invention provides a cyclic peptide comprising thestructure:

wherein X is selected from the group consisting of an amino acid, anamino acid analog, a peptidomimetic and a non-anilde isostere, Z isselected from the group consisting of a synthetic amino acid and abiosynthetic amino acid, R is selected from the group consisting ofoxygen, nitrogen, sulfur and carbon, n is 0 to 10 and y is 1 to 10.

The present invention also provides a cyclic peptide comprising theamino acid sequence of NH₂—X_((n))-Z-X_((y))—COOH and a cyclic bondbetween the Z residue and COOH other than a thioester bond, wherein X isselected from the group consisting of an amino acid, an amino acidanalog a peptidomimetic and a non-amide isostere. Z is selected from thegroup consisting of a synthetic amino acid and a biosynthetic aminoacid, n is 0 to 10 and y is 1 to 10.

An embodiment of the present invention is a compound comprising theprovided peptide, peptidomimetic thereof or polymer thereof.

A further embodiment of the invention extends to a method for thepreparation of the present cyclic peptide, which method comprisesassembling the linear constituents of the peptide under preparation on aPEGA resin support to form a protected and bound peptide chain; treatingthe resulting peptide chain to cause deprotection thereof, thereaftertreating the deprotected peptide with buffer at a neutral pH for aperiod of time sufficient to cleave said peptide from said solid phasesupport and to form the cyclic peptide in object; and recovering thecyclic peptide. More particularly the method comprises assembling thelinear peptide chain corresponding in composition to the said cyclicpeptide on to a solid phase resin support containing3-mercapto-propionamide-polyethyleneglycol-poly-(N₁N₄-dimethacrylamide)(HS-PEGA) to form a protectedassembled peptide; treating the protected assembled peptide of theprevious step to deprotect the said assembled peptide; treating thedeprotected peptide with aqueous buffer at a pH of about 7.0 for aperiod of time sufficient to form the said cyclic peptide and to cleavethe peptide from the solid phase resin support; and recovering thecyclic peptide in object.

As described in detail in Example 1 and as depicted in FIG. 1A herein,the present method utilizes a solid phase cyclization protocol as itslast step in the formation of the inventive cyclic peptides. Also, themethod involved the initial preparation of a fully unprotected peptideon a solid support through a reactive thiol ester bond. Accordingly, arepresentative solid phase resin support suitable for use in the presentmethod may comprise BOC-AA-(linear assembled peptide)-PEGA. Further, thedeprotection treatment that follows the assembly of the peptide on theresin support may for example, be performed with HF for a period of timeof about 1 hour. Thereafter, the cleavage of the peptide from thesupport and the formation of the cyclic peptide may be performed with abuffer such as Na₂PO₄ and acetonitride. Also, this step is performed fora period of time sufficient to achieve both cleavage and cyclization,which may-for example, extend for a period of about 12 hours. Naturallythe foregoing reagents and process parameters may vary within the scopeof the invention, and the invention is intended to cover such variationswithin its spirit and scope.

In another embodiment of this invention, the cyclic peptide is capableof inhibiting agr response. In another embodiment of this invention. Zhas a side chain comprising oxygen or nitrogen. In another embodiment ofthis invention. Z presents a functionality capable of cyclizing througha thioether group, an ether group or a carbon-carbon group. In yetanother embodiment of this invention, the cyclic bond is a lactam orlactone bond. In still another embodiment, y is 4. According to yetanother embodiment of this invention, the peptide has an amino acidsequence that comprises G-V-N-A-X-S-S-L-F (Seq.ID No.:1).G-A-N-A-X-S-S-L-F (Seq.ID No.:2), G-V-A-A-X-S-S-L-F (Seq.ID No.:3).A-V-A-N-X-S-S-L-F (Seq.ID No.:4), G-V-N-A-X-A-S-L-F (Seq.ID No.:5),G-V-N-A-X-S-A-L-F (Seq.ID No.:6), G-V-N-A-X-S-S-A-F (Seq.ID No.:7), andX-S-S-L-F (Seq.ID No. 8). Still, in yet another embodiment of thepresent invention, the peptide has an amino acid sequence that comprisesa hydrophobic amino acid in the carboxy terminal or penultimatecarboxyterminal position.

The present invention also provides a pharmaceutical compositioncomprising the described peptide and a pharmaceutically acceptablecarrier. In an embodiment of this invention, the carrier is selectedfrom the group consisting of a diluent, an aerosol, a topical carrier,an aqueous solution, a nonaqueous solution and a solid carrier.

Finally, the present invention provides a method for treating S. aureusinfection in a subject comprising administering to the subject an amountof the provided pharmaceutical composition in an amount effective totreat the infection.

As used herein, “pharmaceutically acceptable” refers to molecularentities and compositions that are physiologically tolerable and do nottypically produce an allergic or similar untoward reaction, such asgastric upset, dizziness and the like, when administered to a human. Apharmaceutically acceptable carrier encompasses any of the standardpharmaceutically accepted carriers, such as phosphate buffered salinesolution, water emulsions such as an oil/water emulsion or atriglyceride emulsion, various types of wetting agents, tablets, coatedtablets and capsules. Typically such carriers contain excipients such asstarch, milk, sugar, certain types of clay, gelatin, stearic acid, talc,vegetable fats or oils, gums, glycols, or other known excipients. Suchcarriers may also include flavor and color additives or otheringredients. The invention also provides for pharmaceutical compositionscapable of inhibiting S. aureus infection together with suitablediluents, preservatives, solubilizers, emulsifiers and adjuvants. Otherembodiments of the compositions of the invention incorporate particulateforms, protective coatings, protease inhibitors or permeation enhancersfor various routes of administration, including but not limited tointravenous, intramuscular, parenteral, pulmonary, nasal and oral.

As used herein, an “effective amount” is the amount required to achievea clinically significant reduction in S. aureus infection preferably ofat least 30 percent, more preferably of at least 50 percent, mostpreferably of at least 90 percent. Accordingly, the effective amountwill vary with the subject being treated, as well as the condition to betreated. For the purposes of this invention, the methods ofadministration are to include but are not limited to administrationcutaneously, subcutaneously, intravenously, parenterally, orally,topically, or by aerosol.

The present invention further contemplates therapeutic compositionsuseful in practicing the therapeutic methods of this invention. Asubject therapeutic composition includes, in admixture, apharmaceutically acceptable excipient (carrier) and one or more of apolypeptide analog or fragment of the provided peptide or peptidecomposition, a peptidomimetic composition thereof as described herein asan active ingredient. A cocktail of the provided pharmaceuticalcomposition in various combinations is also contemplated.

The preparation of therapeutic compositions which contain polypeptides,analogs or active fragments as active ingredients is well understood inthe art. Typically, such compositions are prepared as injectables,either as liquid solutions or suspensions, however, solid forms suitablefor solution in, or suspension in, liquid prior to injection can also beprepared. The preparation can also be emulsified. The active therapeuticingredient is often mixed with excipients which are pharmaceuticallyacceptable and compatible with the active ingredient. Suitableexcipients are, for example, water, saline, dextrose, glycerol, ethanol,or the like and combinations thereof. In addition, if desired, thecomposition can contain minor amounts of auxiliary substances such aswetting or emulsifying agents, pH buffering agents which enhance theeffectiveness of the active ingredient.

A polypeptide, analog or active fragment can be formulated into thetherapeutic composition as neutralized pharmaceutically acceptable saltforms. Pharmaceutically acceptable salts include the acid addition salts(formed with the free amino groups of the polypeptide or antibodymolecule) and which are formed with inorganic acids such as, forexample, hydrochloric or phosphoric acids, or such organic acids asacetic, oxalic, tartaric, mandelic, and the like. Salts formed from thefree carboxyl groups can also be derived from inorganic bases such as,for example, sodium, potassium, ammonium, calcium, or ferric hydroxides,and such organic bases as isopropylamine, trimethylamine, 2-ethylaminoethanol, histidine, procaine, and the like.

The therapeutic polypeptide-, analog- or active fragment-containingcompositions are conventionally administered intravenously, as byinjection of a unit dose, for example. The term “unit dose” when used inreference to a therapeutic composition of the present invention refersto physically discrete units suitable as unitary dosage for humans, eachunit containing a predetermined quantity of active material calculatedto produce the desired therapeutic effect in association with therequired diluent; i.e., carrier, or vehicle.

The compositions are administered in a manner compatible with the dosageformulation, and in a therapeutically effective amount. The quantity tobe administered depends on the subject to be treated, capacity of thesubject's immune system to utilize the active ingredient, and degree ofinhibition desired. Precise amounts of active ingredient required to beadministered depend on the judgment of the practitioner and are peculiarto each individual. However, suitable dosages may range from about 0.1to 20, preferably about 0.5 to about 10, and more preferably one toseveral, milligrams of active ingredient per kilogram body weight ofindividual per day and depend on the route of administration. Suitableregimes for initial administration and booster shots are also variable,but are typified by an initial administration followed by repeated dosesat one or more hour intervals by a subsequent injection or otheradministration. Alternatively, continuous intravenous infusionsufficient to maintain concentrations of ten nanomolar to ten micromolarin the blood are contemplated.

As used herein, “pM” means picomolar, “nM” means nanmolar, “uM, meansmicromolar, “mM” means millimolar, “ul” or “μl” mean microliter, “ml”means milliliter, “l” means liter.

As used herein, the term “synthetic amino acid” means an amino acidwhich is chemically synthesized and is not one of the 20 amino acidsnaturally occurring in nature.

As used herein, the term “biosynthetic amino acid” means an amino acidfound in nature other than the 20 amino acids commonly described andunderstood in the art as “natural amino acids.” Examples of “non-amideisosteres” include but are not limited to secondary amine, ketone,carbon-carbon, thioether, and ether moieties.

As used herein, the term “non-natural peptide analog” means a variantpeptide comprising a synthetic amino acid.

As used herein, amino acid residues are preferred to be in the “L”isomeric form. However, residues in the “D” isomeric form can besubstituted for any L-amino acid residue, as long as the desiredfunctional property of immunoglobulin-binding is retained by thepolypeptide. NH₂ refers to the free amino group present at the aminoterminus of a polypeptide. COOH refers to the free carboxy group presentat the carboxy terminus of a polypeptide. Abbreviations for amino acidresidues are used in keeping with standard polypeptide nomenclaturedelineated in J. Biol. Chem., 243:3552-59 (1969).

It should be noted that all amino-acid residue sequences are representedherein by formulae whose left and right orientation is in theconventional direction of amino-terminus to carboxy-terminus.Furthermore, it should be noted that a dash at the beginning or end ofan amino acid residue sequence indicates a peptide bond to a furthersequence of one or more amino-acid residues.

Amino acids with nonpolar R groups include: Alanine. Valine, Leucine,Isoleucine, Proline, Phenylalanine, Tryptophan and Methionine. Aminoacids with uncharged polar R groups include: Glycine, Serine, Threonine,Cysteine, Tyrosine, Asparagine and Glutamine. Amino acids with chargedpolar R groups (negatively charged at Ph 6.0) include: Aspartic acid andGlutamic acid. Basic amino acids (positively charged at pH 6.0) include:Lysine, Arginine and Histidine (at pH 6.0). Amino acids with phenylgroups include: Phenylalanine, Trptophan and Tyrosine. Particularlypreferred substitutions are: Lys for Arg and vice versa such that apositive charge may be maintained; Glu for Asp and vice versa such thata negative charge may be maintained; Ser for Thr such that a free —OHcan be maintained; and Gln for Asn such that a free NH₂ can bemaintained. Amino acids can be in the “D” or “L” configuration. Use ofpeptidomimetics may involve the incorporation of a non-amino acidresidue with non-amide linkages at a given position.

Amino acid substitutions may also be introduced to substitute an aminoacid with a particularly preferable property. For example, a Cys may beintroduced a potential site for disulfide bridges with another Cys. AHis may be introduced as a particularly “catalytic” site (i.e., His canact as an acid or base and is the most common amino acid in biochemicalcatalysis). Pro may be introduced because of its particularly planarstructure, which induces β-turns in the protein's structure. Thefollowing examples are presented in order to more fully illustrate thepreferred embodiments of the invention. They should in no way beconstrued, however, as limiting the broad scope of the invention. Whilethe invention is described and illustrated herein by references tovarious specific material, procedures and examples, it is understoodthat the invention is not restricted to the particular materialcombinations of material, and procedures selected for that purpose.Numerous variations of such details can be implied as will beappreciated by those skilled in the art.

EXAMPLES Example 1 Synthesis of a Novel Class of Peptides Responsiblefor S. aureus Bacterial Interference

The initial synthetic route to the AgrD thiololactone peptides,involving the solution-based cyclization of a thiol ester precursor,proved problematic due to the difficulties associated with the synthesisof the linear starting material. A more efficient strategy was thusdeveloped which involved solid-phase cyclization as the final syntheticstep (FIG. 1A). Key to this process was the ability to prepare a fullyunprotected peptide immobilized on a solid-suppport through a reactivethiol ester bond. This was achieved using the recently described3-mercaptopropionamide-polyethylene glycol-poly-(N,N-dimethylacrylamide)[HS-PEGA] support (Camarero, J. A., 1998) in combination with Boc-solidphase peptide synthesis (SPPS) (Schnolzer, M., et al., 1992). The acidstability of the alkyl-thiol ester linkage between the peptide and theresin means that the completed peptide can be globally deprotectedwithout being cleaved from the support. Generation of the desiredthiololactone-peptide is then achieved by simply swelling thepeptide-resin beads in aqueous buffer at pH 7.0, resulting in achemoselective intramolecular cyclizatioilcleavage reaction. Note thatthis final step is made possible due to the excellent swellingproperties of the PEGA support in water (Mendal, M., 1992).

The synthetic approach illustrated in FIG. 1A was used to preparepeptides AgrDI and AgrDII from S. aureus group I and group II strains,respectively (The amino acid sequence of the group III AgrD peptide hasnot yet been established at the time of the present invention). In eachcase, the final cyclization/cleavage reaction was found to be remarkablyclean giving rise to a single major component in excellent yield (FIG.1B). Following purification, the ligation products were characterized asbeing the expected thiololactone-peptides by electrospray massspectrometry, chemical reactivity to neutral hydroxylamine (Chou, T. C.and Lipmann. F, 1952) and two-dimensional ¹H nuclear magnetic resonance(NMR) spectroscopy (Bax, A., et al., 1985; Wuthrich, K, 1986). (Peptidethiol esters react rapidly with neutral hydroxylamine to give thecorresponding hydroxamate derivatives).

The biological activity of the synthetic AgrDI and AgrDII peptides wasassayed using cultured S. aureus strains containing a β-lactamasereporter gene fused to the agrP3 promoter (Novick, R. P., et al., 1995).This allowed activation or inhibition of the agr response to bemonitored spectrophotometrically using a calorimetric β-lactamaseactivity assay (Table 1). As with their naturally derived counterparts,synthetic AgrDI and AgrDII were found to activate the agr response onlywithin their own S. aureus class, and inhibit the agr response only inS. aureus strains from the other two classes (Table 1). Further studiesrevealed a dose-dependent relationship between the amount of peptideadded to the culture supernatant and the degree of activation/inhibitionof the agr response (FIGS. 2A-2B). Analysis of the resulting sigmoidalresponse curves indicated that the ED50 and IC50 values, for activationand inhibition the agr response respectively, were in the low nanomolarrange (Table 1). Moreover, these data indicate that there is a criticalthreshold concentration of the AgrD peptide required for activation ofthe agr response. This is consistent with thedensitysensing/autoinduction mechanism previously proposed (Ji, G., etal., 1997). Importantly, no activation/inhibition activity was detectedwith linear carboxylate synthetic peptides corresponding to the AgrDIand AgrDII sequences, even at high μM concentrations (Table 1).

TABLE 1 BIOLOGICAL ACTIVITY OF SYNTHETIC AgrD PEPTIDES ED₅₀ Activation(nM) IC₅₀ Inhibition (nM) S. aureus Group S. aureus Group PEPTIDE I IIIII I II III

10.2 No Activation No Activation No Inhibition 2.9 3.2

No Activation 3.6 No Activation 3.4 No Inhibition 3.1

No Activation No Activation No Activation No Inhibition No Inhibition NoInhibition

No Activation No Activation No Activation No Inhibition No Inhibition NoInhibition

No Activation No Activation No Activation 7.9 No Inhibition n/d

No Activation No Activation No Activation 0.21 No Inhibition n/dThat biological activity is restricted to the thiololactone-peptides,serves to confirm that this unusual posttranslational modification ispresent within the secreted AgrD peptides.

Example 2 Functional Significance of the Cyclic Ring Structure

The precision and convenience of the synthetic approach makes itpossible to systematically vary the chemical structure of the peptides,thus enabling detailed structure-activity studies to be performed. Withrespect to the AgrD peptides, the initial focus was on the followingquestions: (i) Which amino acids within the sequence are most importantfor affinity/selectivity? (ii) What is the role of the thiololactoneunit in activation and inhibition of the agr response? To address thefirst of these issues, an alanine scan was performed on the group IIAgrD peptide. Each of the alanine-modified AgrDII peptide variants wasprepared and characterized as before, and in each case the purifiedpeptide assayed for its ability to activate or inhibit the agr responsein each of the three S. aureus strains. Analysis of the resultssummarized in FIG. 2C, reveals that there are certain amino acids,residing both within the ring and the tail of the molecules, which arecritical for the activation of the agr response (Asn-3,-Leu-8, Phe-9).The alanine mutant peptides exhibit a wide activation profile, showingboth increases and decreases in activity. In contrast, inhibition of theagr response appears to depend on amino acids only in the ring (Leu-8,Phe-9) and all of the inhibitory, alanine-modified AgrDII peptidesexhibit increased activity as compared to the wildtype.

The functional significance of the thiololactone structure in the AgrDpeptides was investigated through the synthesis of a series of AgrDIIvariants (Table 1). To address whether a cyclic thiol ester group isstrictly required for activity in the native peptide, a linear thiolester analogue of AgrDII was prepared and assayed (see, ExperimentalProcedures for detail). As with the linear carboxylate AgrDII variantdescribed earlier, the linear thiol ester peptide was unable to eitheractivate or inhibit the agr response even when added to cultured cellsat μM concentrations. This result suggests that the cyclic structurepresent-within the AgrD peptides is indispensable for biologicalactivity.

Example 3 Lactone and Lactam Variants in the Cyclic Ring StructureProvide Peptides Capable of Inhibitory Activity Without ActivationActivity

Thiol ester groups are moderately good acylating agents, a propertywhich is utilized in several biological processes (Law, S. K. and A. W.Dodds. 1997; Xu, M.-Q., and F. B. Perter, 1996; Porter, J. A., et al.,1996). It is intriguing to speculate that upon receptor binding, thethiololactone present in the AgrD peptides serves as an acyl donor forthe covalent modification of a specific residue within AgrC. The effectof replacing the thiololactone unit in AgrDII with both ester (lactone)and amide moieties (lactam) was of interest. In principle, both of thesevariants should be significantly less reactive than the thioesterpeptide ( ), while the lactone variant of AgrDII should also beisosteric to wildtype. Synthesis of the desired AgrDII lactone andlactam variants was achieved via solution cyclization of a partiallyprotected intermediate, followed by global side-chain deprotection. Inparticular, thiol esters are significantly more reactive towardsnitrogen nucleophiles than oxygen esters (Bruice, T. C. and S. J.Benkovic, 1966). As with the linear peptides described above, both thepurified lactone and lactam variants were unable to activate the agrresponse in any of the three S. aureus strains (Table 1). However, bothvariants are able to inhibit the agr response in groups I and III S.aureus strains. Clearly, the reactive thioester bond is necessary forthe activation of the agr response in vivo, however it is not necessaryfor inhibition.

Analysis of the biological properties of the various AgrDII peptidevariants prepared in this study reveals the following: (i) Activation ofthe agr response is extremely sensitive to both the amino acid sequenceand the chemical/stereochemical nature of the AgrD peptide; (ii)Inhibition of the agr response is sensitive to the backbonestereochemistry and the amino acid sequence of the AgrD peptide, but isnot affected by changes in the chemical reactivity of the cycliclinkage. These observations suggest that activation and inhibition ofthe agr response occur through two different mechanisms.

The synthesis of virulence factors and other extracellular proteinsresponsible for pathogenicity in Staphylococcus aureus is under thecontrol of the agr locus. A secreted agr-encoded peptide, AgrD, is knownto be an effector of self-strain activation and cross-strain inhibitionof this agr response. Preliminary analysis of AgrD peptides isolatedfrom cultrue supernatants, suggested that they contain an unusual thiolester-linked cyclic structure. In the present invention, chemicalsynthesis confirms that these AgrD peptides contains a thiololactoneunit, and that this structure is absolutely necessary for fullbiological activity in the native peptides. Structure-function studiesprovided by the present invention identify and elucidate key aspects ofthe peptide structure involved in the differential activation andinhibition functions of the peptides. Novel., non-natural peptidevariants are also provided which exhibit no activation activity whileretaining (or enhancing) inhibitory activity. Peptides having suchproperties are useful for treating S. aureus infections.

Discussion

One proposed model in which an AgrD peptide binds its own AgrC receptor(i.e. from the same S. aureus class) in a different manner to an AgrCreceptor from an another class is illustrated in FIG. 3. This mayinvolve two slightly different orientations of the peptide within thereceptor binding pocket, although more than one discrete binding sitewithin the AgrC receptor cannot be excluded. It is further hypothesizedthat in the intra-class association, highly specific side-chaininteractions between AgrC and AgrD result in the thiol ester linkage ofthe peptide being positioned adjacent to a nucleophilic group within thereceptor. This juxtaposition leads to a trans-acylation reaction andactivation of the agr response through an associated conformation changein the receptor. The thiol ester linkage is a sufficiently reactivemoiety to participate in this trans-acylation step and would explain itspresence within the AgrD peptide rather than one of the more commonstrategies for stereochemical restraint such as a disulfide- oramide-bond formation.

In contrast, no such juxtaposition would be present in the interclassreceptor-ligand interaction due to the absence of these specificinteractions. Thus the inhibition of the agr response would not involvea signal-transducing trans-acylation step, but rather a non-covalentbinding interaction which would serve to exclude the strain's ownautoinducing AgrD peptide from the receptor binding pocket. Thisnon-covalent binding interaction does require specific residues, asdemonstrated in the alaninescanning mutagenesis results. It is pertinentto note that the lactone and lactam variants, while being able toinhibit in the appropriate inter-class fashion, do not inhibit self.Inhibition by default, therefore, does not occur when a strain's ownautoinducing lactone/lactam variant encounters its own receptor. Thisevidence further supports the proposed model in which activation andinhibition occur through discrete mechanisms.

In summary, chemical synthesis has been used to confirm the presence ofan thiololactone structure within secreted AgrD autoinducing peptides.This highly unusual post-translational modification appears to bemandatory for full biological activity. Based on initialstructure-activity studies, it is argued that the thiol esterfunctionality undergoes a trans-acylation reaction with a specificnucleophile in the AgrC receptor, and that this chemical step isrequired for activation (but not inhibition) of the agr response. It isalso likely that the thiololactone unit limits the in vivo half-life ofthe peptide-the thiol ester linkage will undergo slow hydrolysis atphysiological pH leading to the generation of an inactive linearpeptide. The biological significance of this short-term in vivo efficacyis as yet unknown. It is equally unknown what role (if any) the recentlyreported 38 KDa RAP protein (Balaban, N., et al., 1998) plays inactivation of the agr response by the secreted AgrD peptides.

Ready synthetic access to AgrD peptides represents an important steptowards using the agr autoinduction system as a route to noveltherapeutic agents. Indeed, the observation that it is possible toprepare novel synthetic AgrD variants which are capable of inhibitingbut not activating the agr response is particularly significant in thisregard. Moreover, the ability to easily adapt a solid-phase syntheticstrategy to combinatorial-type synthesis is advantageous in the rapididentification of interesting compounds.

Experimental Procedures:

Biological activity of sythetic AgrD peptide. Biological assays wereperformed using groups I (RN6390B), II (SA502A) and III (RN8463) S.aureus strains (Ji, G., et al., 1997), each containing an agr P3-blazfusion plasmid (Novick, R. P., et al., 1995). Cells were grown in CYGPmedium at 37° C. to either early exponential phase for agr activationstudies, or midexponential phase for agr inhibition studies. To thecultured cells were then added either buffer solution (negativecontrol), the appropriate cell supernatant containing the natural AgrDpeptide as prepared as in (Ji, G., et al., 1995) (positive control) orthe synthetic peptide solution in 20 mM tris.HCl buffer at pH 6.0. Thecultures were then incubated at 37° C. with shaking for either 55minutes (activation) or 80 minutes (inhibition) and β-lactamase activitythen assayed using the nitrocefin spectrophotometric method modified asdescribed in (Novick, R. P., et al., 1995) ED₅₀ and IC₅₀ values wereextracted from the sigmoidal dose-response curves (e.g. FIGS. 2A-2B)using the program PRISM (GRAPHPAD Software Inc., San Diego, Calif.). Allassays were performed in triplicate and the ED₅₀ and IC₅₀ values agreedto within ±10%.

Thioesterification Studies:

Initial studies involved selective thioesterification of a linearα-thiol acid peptide with 5,5′-dithiobis(2-nitrobenzoic acid) to givethe S-(5-sulfenyl-2-nitrobenzoic acid) α-thiol ester derivative. Thislinear thiol ester precursor was then cyclized in solution throughtransthioesterification involving the cyteine sulfhydryl group. Theoverall yields using this strategy were poor, principally because ofdifficulties in selectively esterifying the α-thiol peptide.

Peptide Synthesis

All peptides were synthesized manually according to the in situneutralization/HBTU activation protocol for Boc SPPS (M. Schnolzer, P.Alewood. A. Jones, D. Alewood, B. H. Kent, Int. J. Pept. Protein Res.40: 180-193 (1992). Thiololactone AgrD peptides were assembled onpre-loaded Boc-AA-[COS]-PEGA resins (Camarero, J. A., et al., 1998).Following chain assembly, peptides were treated with HF for 1 hour at 0°C. to give the corresponding fully unprotected peptide-[COS]-PEGA resinswhich were then washed with cold diethyl ether and then CH₃CN/H₂Ocontaining 0.1% trifluoroacetic acid. Unprotected peptides werecliemoselectively cyclized and simultaneously cleaved from the supportby swelling the beads in a mixtture of 0.1 M sodium phosphate buffer atpH 7.0 and acetonitrile (80:20). After 12 hours rection, the beads wereremoved by filtration, washed with 0.1% trifluoroacetic acid in waterand the peptides purified from the filtrate by reverse-phase HPLC.

Assembly of Peptides on Resin.

The peptide GVNAASSLF was assembled on an HS-PEGA resin (Camarero, etal., 1998) using Boc-SPPS. This corresponds to the AgrDII sequence withthe single cysteine residue mutated to an alanine. Following synthesisand global deprotection, the peptide-[COS]-PEGA beads were swollen in abuffer containing 0.1 M sodium phosphate, pH 7.0 aid ethanethiol (2%v/v), and the cleavage reaction allowed to proceed for 3 hours. Thedesired ethyl a thiol ester peptide was then purified from thesupernatant by reverse-phase HPLC.

Protected Peptides

The protected peptidesZ-Gly-Val-Asn-Ala-Ser(¹Bu)-Ser(Bzl)-Ser(Bzl)-Leu-Phe andZ-Gly-Val-Asn-Ala-Dapa(Boc)-Ser(Bzl)-Ser(Bzl)-Leu-Phe corresponding tothe AgrDII sequence with a Cys5 to Ser mutation (lactone) and a Cys5 toDapa (Diaminopropionic acid) (lactam) respectively, were synthesized ona Wang-resin using an Fmoc Nα protection strategy with HBTU activationprotocols. Following chain assembly, the peptides were cleaved from thesupport and the Ser-5 or Dapa-5 side-chain deprotected by treatment witha trifluoroacetic acid: anisole: water mixture (90:5:5) for 4 hours. Thepartially protected peptide-αcarboxylates were then dissolved in DMF(0.5 mg/mL) and treated with PyBOP (5 eq.) (and a catalytic amount ofdimethylaminopyridine for the lactone precursor). The cyclizationreaction was monitored by HPLC which indicated a period of 2 hours to besufficient for complete reaction. The remaining protecting groups werethen removed by treatment with HF and the desired peptides purified byreverse-phase HPLC and characterized by mass spectometry and 2D ¹H NMRspectroscopy.

NMR

Two-dimensional ¹H NMR spectra were measured on a Bruker DPX-400spectrometer. Peptides were dissolved in either dimethylsulfoxide-d6 or9:1 H2O/D2O pH 4.0 to a final concentration of 1-2 mM and a series ofTOCSY (A. Bax, D. G. Davis, J. Magn. Reson. 65: 355-360 (1985) and ROESYexperiments recorded at 278 K. ¹H resonances were assigned usingstandard procedures (K. Wuthrich, NMR of Proteins and Nucleic Acids(Wiley, N.Y., 1986).

REFERENCES

The following is a list of documents related to the above disclosure andparticularly to the experimental procedures and discussions. Thedocuments should be considered as incorporated by reference in theirentirety.

-   1. Balaban. N., et al., Science 280:438-440 (1998).-   2. Bax. A. and D. Q. Davis. J. Magn. Reson. 655:355-360 (1985)-   3. Buice, T. C. and S. J. Benkovic, in Bioorganic Mechanisms    1:259-297 (Benjamin, N.Y., 1966).-   4. Camarero, G. C., et al., J. Peptide Res. 51:303-316 (1998).-   5. Chou, T. C. and F. Lippmann, J. Biol. Chem. 196:89 (1952).-   6. Ji, G., et al., Proc. Natl. Acad. Sci. USA 92:12055-12059 (1995).-   7. Ji, G., et al., Science 276:2027-2030 (1997).-   8. Law, S. K., and A. W. Dodds, Protein Science 6:263-274 (1997).-   9. Mendal, M. Tetrahedron Lett. 33:3077-3080 (1992).-   10. Morfeldt, E., etal., EMBO J. 14:4569-4577 (1995).-   11. Muir, T. W., et al., Chemistry and Biology 3:817-825 (1996).-   12. Novick, R. P., et al., Mol. Gen. Genet. 248:446-458 (1995).-   13. Novick, R. P., et al., EMBO J. 12:3967-3975 (1993).-   14. Porter, J. A., et al., Science 274:255-259 (1996).-   15. Sclnolzer, M., et al., Int. J. Pept. Protein Res. 40:180-193    (1992).-   16. Wuthrich, K, NMR of Proteins and Nucleic Acids (Wiley, N.Y.,    1986).-   17. Xu, M.-Q., and F. B. Perler, EMBO J. 15:5146-5153 (1996).

This invention may be embodied in other forms or carried out in otherways without departing from the spirit or essential characteristicsthereof. The present disclosure is therefore to be considered as in allrespects illustrative and not restrictive, the scope of the inventionbeing indicated by the appended Claims, and all changes which comewithin the meaning and range of equivalency are intended to be embracedtherein.

1. A cyclic peptide comprising the structure: wherein X is selected fromthe group consisting of an amino acid, an amino acid analog,

a peptidomimetic and a non-amide isostere, Z is selected from the groupconsisting of a synthetic amino acid and a biosynthetic amino acid, R isselected from the group consisting of oxygen, nitrogen, sulfur andcarbon, n is 0 to 10 and y is 1 to 10, wherein the cyclic peptideinhibits the accessory gene regulator (agr) response.
 2. A cyclicpeptide comprising the amino acid sequence of NH₂—X_((n))-Z-X_((y))—COOHand a cyclic bond between the Z residue and COOH other than a thioesterbond, wherein X is selected from the group consisting of an amino acid,an amino acid analog, a peptidomimetic and a non-amide isostere, Z isselected from the group consisting of a synthetic amino acid and abiosynthetic amino acid, n is 0 to 10 and y is 1 to 10, wherein thecyclic peptide inhibits the accessory gene regulator (agr) response. 3.A method for treating a Staphylococcus aureus (S. aureus) infection in asubject comprising administering to the subject an amount of a cyclicpeptide effective to treat the infection, said cyclic peptide comprisingthe structure:

wherein X is selected from the group consisting of an amino acid, anamino acid analog, a peptidomimetic and a non-amide isostere, Z isselected from the group consisting of a synthetic amino acid and abiosynthetic amino acid, R is selected from the group consisting ofoxygen, nitrogen, sulfur and carbon, n is 0 to 10 and y is 1 to 10,wherein said cyclic peptide is administered cutaneously, subcutaneously,intravenously, parenterally, orally, topically, or by aerosol in aneffective amount to achieve a clinically significant reduction in saidS. aureus infection.
 4. A method for treating a Staphylococcus aureus(S. aureus) infection in a subject comprising administering to thesubject an amount of a cyclic peptide effective to treat the infection,said cyclic peptide comprising the amino acid sequence ofNH₂—X_((n))-Z-X_((y))—COOH and a cyclic bond between the Z residue andCOOH other than a thioester bond, wherein X is selected from the groupconsisting of an amino acid, an amino acid analog, a peptidomimetic anda non-amide isostere, Z is selected from the group consisting of asynthetic amino acid and a biosynthetic amino acid, n is 0 to 10 and yis 1 to 10, wherein said cyclic peptide is administered cutaneously,subcutaneously, intravenously, parenterally, orally, topically, or byaerosol in an effective amount to achieve a clinically significantreduction in said S. aureus infection.
 5. The method of claim 3, whereinZ has a side chain comprising oxygen, nitrogen or carbon.
 6. The methodof claim 4, wherein Z has a side chain comprising oxygen, nitrogen orcarbon.
 7. The method of claim 4, wherein the cyclic bond is a lactam orlactone bond.
 8. The method of claim 3, wherein the cyclic peptideinhibits the agr response.
 9. The method of claim 4, wherein the cyclicpeptide inhibits the agr response.
 10. The method of claim 3, wherein yis
 4. 11. The method of claim 4, wherein y is
 4. 12. The method of claim10, wherein the peptide is selected from the group of peptides having anamino acid sequence that comprises G-V-N-A-X-S-S-L-F (SEQ ID NO: 1),G-A-N-A-X-S-S-L-F (SEQ ID NO: 2), G-V-A-A-X-S-S-L-F (SEQ ID NO: 3),A-V-A-N-X-S-S-L-F (SEQ ID NO: 4), G-V-N-A-X-A-S-L-F (SEQ ID NO: 5),G-V-N-A-X-S-A-L-F (SEQ ID NO: 6), G-V-N-A-X-S-S-A-F (SEQ ID NO: 7) andX-S-S-L-F (SEQ ID NO: 8).
 13. The method of claim 11, wherein thepeptide is selected from the group of peptides having an amino acidsequence that comprises G-V-N-A-X-S-S-L-F (SEQ ID NO: 1),G-A-N-A-X-S-S-L-F (SEQ ID NO: 2), G-V-A-A-X-S-S-L-F (SEQ ID NO: 3),A-V-A-N-X-S-S-L-F (SEQ ID NO: 4), G-V-N-A-X-A-S-L-F (SEQ ID NO: 5),G-V-N-A-X-S-A-L-F (SEQ ID NO: 6), G-V-N-A-X-S-S-A-F (SEQ ID NO: 7) andX-S-S-L-F (SEQ ID NO: 8).
 14. The method of claim 3, wherein acomposition is administered and said composition comprises said peptideand a carrier.
 15. The method of claim 4, wherein a composition isadministered and said composition comprises said peptide and a carrier.16. The method of claim 3, wherein a pharmaceutical composition isadministered and said pharmaceutical composition comprises said peptideand a pharmaceutically acceptable carrier.
 17. The method of claim 4,wherein a pharmaceutical composition is administered and saidpharmaceutical composition comprises said peptide and a pharmaceuticallyacceptable carrier.
 18. The pharmaceutical composition of claim 16,wherein the carrier is selected from the group consisting of a diluent,an aerosol, a topical carrier, an aqueous solution, a nonaqucoussolution, and a solid carrier.
 19. The pharmaceutical composition ofclaim 17, wherein the carrier is selected from the group consisting of adiluent, an aerosol, a topical carrier, an aqueous solution, anonaqucous solution, and a solid carrier.